Dendrogram
Centroid Linkage Circular Dark
Centroid method clustering displayed as circular dendrogram
Output
Python
import matplotlib.pyplot as plt
import numpy as np
from scipy.cluster.hierarchy import dendrogram, linkage, set_link_color_palette
np.random.seed(369)
n = 18
labels = [f'N{i}' for i in range(1, n+1)]
data = np.random.rand(n, 6) * 85
Z = linkage(data, method='centroid')
fig_temp, ax_temp = plt.subplots()
set_link_color_palette(['#27D3F5', '#F5276C', '#6CF527', '#F5D327', '#5314E6'])
dn = dendrogram(Z, labels=labels, no_plot=False, color_threshold=0.55*max(Z[:,2]),
above_threshold_color='#555555', ax=ax_temp)
plt.close(fig_temp)
icoord = np.array(dn['icoord'])
dcoord = np.array(dn['dcoord'])
colors = dn['color_list']
x_min, x_max = icoord.min(), icoord.max()
y_max = dcoord.max()
def to_polar(x, y):
theta = (x - x_min) / (x_max - x_min) * 2 * np.pi * 0.93 + np.pi * 0.035
r = y / y_max * 0.5 + 0.45
return theta, r
fig, ax = plt.subplots(figsize=(10, 10), subplot_kw={'projection': 'polar'}, facecolor='#0a0a0f')
ax.set_facecolor('#0a0a0f')
# Draw rings
for r in [0.55, 0.7, 0.85, 0.95]:
circle_theta = np.linspace(0, 2*np.pi, 100)
ax.plot(circle_theta, [r]*100, color='#27D3F5', linewidth=0.5, alpha=0.2)
for ic, dc, color in zip(icoord, dcoord, colors):
thetas, rs = [], []
for x, y in zip(ic, dc):
t, r = to_polar(x, y)
thetas.append(t)
rs.append(r)
for lw, alpha in [(4, 0.15), (2, 0.9)]:
ax.plot([thetas[0], thetas[1]], [rs[0], rs[1]], color=color, linewidth=lw, alpha=alpha)
ax.plot([thetas[2], thetas[3]], [rs[2], rs[3]], color=color, linewidth=lw, alpha=alpha)
if thetas[1] != thetas[2]:
arc_thetas = np.linspace(min(thetas[1], thetas[2]), max(thetas[1], thetas[2]), 45)
ax.plot(arc_thetas, [rs[1]]*len(arc_thetas), color=color, linewidth=lw, alpha=alpha)
leaf_positions = np.linspace(x_min, x_max, n)
for i, (pos, label) in enumerate(zip(leaf_positions, dn['ivl'])):
theta, _ = to_polar(pos, 0)
rotation = np.degrees(theta) - 90 if np.pi/2 < theta < 3*np.pi/2 else np.degrees(theta) + 90
ha = 'right' if np.pi/2 < theta < 3*np.pi/2 else 'left'
ax.text(theta, 0.32, label, ha=ha, va='center', fontsize=8, color='white',
rotation=rotation, rotation_mode='anchor')
color = ['#27D3F5', '#F5276C', '#6CF527', '#F5D327', '#5314E6'][i % 5]
ax.scatter(theta, 0.45, c=color, s=45, zorder=5, edgecolor='white', linewidth=0.5)
ax.set_ylim(0, 1.02)
ax.set_yticklabels([])
ax.set_xticklabels([])
ax.spines['polar'].set_visible(False)
ax.grid(False)
ax.set_title('Centroid Linkage - Circular View', fontsize=14, color='white', fontweight='bold', y=1.08)
plt.tight_layout()
plt.show()
Library
Matplotlib
Category
Statistical
More Dendrogram examples
☕